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Evolving Molecular Machines: The Plant Edition

Over at Thoughtomics, Lucas has a post up about the evolution of mitochondrial import systems. He starts by going back in time two billion years:

"Life was well underway at the time, with proto-bacteria already populating the oceans for over hundreds of millions of years. One of the cells alive at the time, swallowed an alpha-proteobacterium. Something remarkable happened: the alpha-proteobacterium did not die but survived in the host cell. Over time, the host and symbiont became to be dependent on each other." That symbiont became a mitochondria.

He gets massive brownie point for writing 'proto-bacteria' rather than bacteria, and it is a very remarkable event to have happened. However from the point of view of a plant, it's only half the story, because plants carry two endosymbionts within them: the mitochondria and the chloroplast.

Their stories are remarkably similar. After becoming engulfed by the surrounding cell, two major things happened to them: First (and it had to be first otherwise major problems would have arisen!) a protein import mechanism arose, creating more communication between the symbiont and the host and allowing things to pass between them. Second, the symbiont lost bits of its genome, transferring them into the nucleus of the surrounding cell to create the cooperative arrangement seen today:

Picture above from the amazing science illustration gallery by California state University. Nucleus is purple, chloroplasts are green, and the mitochondria are orange.

Lucas'spost covered the evolution of the import mechanism for the mitochondria. I'm going to write about the same thing, but for chloroplasts. After all, the plants already have mitochondria so they can't use exactly the same import process, they have to be able to differentiate between the two.

Like mitochondria, the chloroplasts are surrounded by two membranes, and outer membrane and an inner membrane. Two transporters are therefore required to get proteins across. In the mitochondria these are called TOM and TIM (Transport of Outer, and Inner Membrane respectively) and in the chloroplasts they are called TOC and TIC, just to keep things simple (Transport of Outer and Inner Chloroplast membrane). They look fairly similar to TIM and TOM, but recognise different sequences attached to the proteins. While the mitochondrial transport machines recognise sequences that contain a lot of the amino acid arginine and form a specific helical shape, the chloroplast machines (TOCand TIC) recognise sequences rich in serine and proline:

TOC and TIC. The proteins of the TOC machine are coloured green, and the TIC machine proteins are all the rest. Diagram from here.

One of the questions that Lucas asks in his post is: where did all of these proteins come from? After all, before you have an endosymbiont, you don't need any kind of apparatus to transport proteins into them. Once you start looking closer at the transport machinery it starts looking suspiciously like a rather rushed and last minute job. Different proteins with different functions have been cobbled together, and while there's still a bit of a debate as to whether these proteins came from the surrounding cell or the endosymbiont I suspect that it may be a bit of both. The cell needs to communicate with the little alien inside it, and once the endosymbiont started loosing genes, it needed a way to keep resources coming in.

So how do you make a protein importer? What do you assemble it from? Plants had a slightly easier task with the chloroplasts as they already had a perfectly serviceable TIM/TOM transporter present. Looking at the TIC complex, the first two components to come in contact with the imported protein (TIC22 and 20, shown in the diagram above in dark purple and orange) show homology to components of the TIM machinery; TIM23 and 17 for anyone interested in the detail. However TIC22 also has far stronger homologues in cyanobacteria, which means it is likely to be a protein owned by the chloroplast, similar to the proteins owned by the mitochondria that got roped in to help with protein import.

The TOC proteins (all green in the diagram above) all appear to have no other function in modern plants other than protein transport. Toc 34 is the GTPase, and as there are many GTPases in cells (used to provide energy) it could have arisen from any one of them. The other TOC proteins are involved in membrane and may have arisen from ancestral membrane receptor proteins, while some components, (including TOC64, not shown above) appear to be rather redundant, as the machinery works perfectly well without them.

The research on this is a little sketchy, there are no good solid biochemical means as yet to discover what might of happened somewhere around two billion years ago in order to create a transport mechanism between the cell and it's organelles. There are plenty of different views out there as well, about where the different subunits might have come from. The only thing that seems clear is that like the mitochondrial import system, this was clearly pulled together from bits of old machinery lying around. It had two billion years to get better after all, and reach the efficiency of the modern-day protein import machines.

@Lab Rat:Really cool that we stumbled upon the same topic. It was bound to happen sometime I guess ;).Just a quick question: does the redundancy of TOC64 also mean that it is a later addition to the chloroplast import machinery, meaning that some in the plant family have it, and some don't?

@Psi: Well, there goes my brownie-point ;).In the defense of that piece, I didn't say a proto-bacterium acquired the endosymbiont (just that they were alive and kicking before this event happened). Knowing myself though, it's an entirely plausible error for me to make, so thanks for the warning and explanation :).

@lucas - I think probably all higher land plants might have TOC64, but it wouldn't surprise me if some protists didn't...might have to check with Psi!

@Psi: GAH I never thought of that! I'm just used to calling everything that was floating around in the biosphere at the dawn of time 'proto-bacteria'. And of course forgot that the things swallowing the future-mitochondrian would already be well on the way to eukaryote by then. Although you have to admit, given that, calling them bacteria would have been even *worse*.

I tend to call anything that was around before things were properly evolved into todays labels 'proto-something'. Just because the often-used phrase "three billion years ago, bacteria..." irritates me so much.